├── Figures ├── McSplicer_summary.pdf ├── McSplicer_summary.png ├── McSplicer_summary.svg └── McSplicer_summary2.png ├── LICENSE ├── README.md ├── bin ├── README.md ├── exonRefine ├── sigcount └── sigcount_pe ├── bin_osx ├── exonRefine └── sigcount ├── examples ├── README.md ├── bam │ ├── ENOPH1_S36.bam │ ├── ENOPH1_S36.bam.bai │ ├── ENOPH1_S5.bam │ └── ENOPH1_S5.bam.bai ├── gtf │ ├── ENOPH1_S36.gtf │ ├── ENOPH1_S36_refined.gtf │ ├── ENOPH1_S5.gtf │ └── ENOPH1_S5_refined.gtf ├── out │ ├── ENSG00000145293_control.csv │ └── ENSG00000145293_mutated.csv ├── run_ENOPH1_gene_example.py └── signature_counts │ ├── ENOPH1_S36.cnt │ └── ENOPH1_S5.cnt ├── python_scripts ├── McSplicer.py ├── add_start_end_read_counts.py ├── cases_code_new.py ├── compute_f00_f01_f10_f11.py ├── compute_frag_length.py ├── compute_ground_truth_tx_abundance.py ├── compute_ground_truth_tx_abundances_toy_examples.py ├── expected_prefix_suffix_length.py ├── generate_sample_cnt_files.py ├── 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